Nucleotide hybridization assays are able to detect sequences of interest, by duplex formation between labeled complementary nucleic acid probes and single stranded nucleic acids targets. Typically, the probes are labeled with radioactivity or enzymes which cleave light- or color-producing molecules. The amplitude of the assay output signal can indicate either the number or merely the presence of target nucleic acids in the sample. However, the output signal is not produced solely by label probes from the formed duplexes, but also from assay imperfections, such as unduplexed label probes that were not removed. A nucleotide hybridization assay includes many steps for sample preparation and assay execution, and at each step, some amount of uncontrollable variation is produced because it is impossible to handle each sample exactly identically. Thus, when a single sample is assayed several times, the results will be variable. The best way to limit this imprecision is to minimize the number of times the sample is manipulated. However, there is a limit to the number of steps that may be eliminated.